More generally, the term "junk DNA" was coined to refer to a specific type of noncoding DNA. These two articles give the historical background for the term:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014423/
https://judgestarling.tumblr.com/post/64504735261/the-origin...
“Junk DNA” is a well accepted term by the scientific community and public.
https://www.scientificamerican.com/article/what-is-junk-dna-...
Humorous take on my point: https://www.amazon.com/Junk-DNA-Journey-Through-Matter/dp/02...
I think my main point was missed which is: “labeling something as non useful and leaving it out of the majority of DNA sequencing as a result has made large swathes of the scientific community unaware of how non coding DNA works within the DNA ecosystem”. I think it’s unfortunate that the community doesn’t label this as “exciting area of unknown science” which would encourage investigation.
This is simply not true. Noncoding RNA and in particular regulatory regions have been known and studied for many decades. The reason we know less about them than about genes has multiple reasons, foremost the difficulty in studying them (large-scale studies have only recently become possible). But it has nothing to do with “ignorance”, or with the label “junk DNA” (the SciAm article you link to is utterly wrong to claim otherwise).
Furthermore, although I also think the name has issues (but mostly in science communication), scientists don’t just “assume” that intergenic, non-regulatory DNA regions are unimportant. They have good reasons, backed by evidence, to think so. I’m actually in the camp that thinks that stochastic biochemical function is potentially important (and I used to study repeat elements) but even so there’s almost certainly very little “exciting … unknown science” in junk DNA.
The majority of research I’ve come across in the past decade has been still focusing on DNA microarrays and qPCR which are focused on coding DNA. Perhaps I’m not seeing all the papers published for the studies you are familiar with and as such have a bias to believe that only a small portion of research is using NGS and is focused on non coding DNA.
1 https://www.yourgenome.org/facts/timeline-history-of-genomic... 2 https://academic.oup.com/hmg/article/25/R2/R157/2198171